8ZCY | pdb_00008zcy

Cryo-EM structure of eSaCas9_NNG-guide RNA-target DNA complex in an interrogation state

• PDB DOI: https://doi.org/10.2210/pdb8ZCY/pdb
• NAKB: 8ZCY
• EM Map EMD-39941: EMDB EMDataResource

• Classification: DNA BINDING PROTEIN
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-04-30 Released: 2025-11-05 
• Deposition Author(s): Omura, S.N., Nakagawa, R., Yamashita, K., Nishimasu, H., Nureki, O.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Engineering a compact high-fidelity Staphylococcus aureus Cas9 variant with broader targeting range and mechanistic insights into its activation.

Omura, S.N., Nakagawa, R., Kajimoto, S., Okazaki, S., Ishiguro, S., Mori, H., Onishi, K., Kashiwakura, Y., Hiramoto, T., Horinaka, K., Tanaka, M., Hirano, H., Jividen, K., Yamashita, K., Tsai, S.Q., Yachie, N., Ohmori, T., Nishimasu, H., Nureki, O.

(2026) Nat Commun 17

• PubMed: 41991526 
• DOI: https://doi.org/10.1038/s41467-026-71626-2
• Primary Citation Related Structures: 
  8ZCY, 8ZCZ, 8ZD0, 8ZDA, 9MB6, 9MB7


• PubMed Abstract: 
  

  Staphylococcus aureus Cas9 (SaCas9) is smaller than the widely used Streptococcus pyogenes Cas9 (SpCas9) and has been harnessed for gene therapy using an adeno-associated virus vector. However, SaCas9 requires a longer NNGRRT (where N is any nucleotide and R is A or G) protospacer adjacent motif (PAM) for target DNA recognition, thereby restricting the targeting range. Although PAM-relaxed Cas9 variants have been developed, expanded targeting is often accompanied by compromised target specificity. Here, we report the rational engineering of eSaCas9-NNG, a SaCas9 variant that recognizes relaxed NNG PAMs while maintaining high target fidelity, thereby overcoming a fundamental trade-off in Cas9-based genome editing. eSaCas9-NNG efficiently induces indels and base conversions at endogenous sites bearing NNG PAMs in human cells and mice, with editing efficiencies comparable to those of other PAM-relaxed nucleases, including SpRY, SpG, and iGeoCas9, but with reduced off-target activity. We further determine the cryo-electron microscopy structures of eSaCas9-NNG in five distinct functional states, revealing the structural basis for its relaxed PAM recognition, improved target specificity, and nuclease activation. Overall, our findings demonstrate that eSaCas9-NNG could be used as a versatile genome editing tool for in vivo gene therapy, and improve our mechanistic understanding of the diverse CRISPR-Cas9 nucleases.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
School of Biomedical Engineering, Faculty of Applied Science and Faculty of Medicine, The University of British Columbia, Vancouver, BC, Canada.
Premium Research Institute for Human Metaverse Medicine (WPI-PRIMe), The University of Osaka, Suita, Osaka, Japan.
Institute for Advanced Biosciences, Keio University, Yamagata, Japan.
Graduate School of Media and Governance, Keio University, Kanagawa, Japan.
Department of Biochemistry, Jichi Medical University School of Medicine, Tochigi, Japan.
Center for Gene Therapy Research, Jichi Medical University, Tochigi, Japan.
Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
Synthetic Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan.
Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Tokyo, Japan. [e-mail].
Inamori Research Institute for Science, Kyoto, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 182.9 kDa 
• Atom Count: 8,307 
• Modeled Residue Count: 790 
• Deposited Residue Count: 1,241 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CRISPR-associated endonuclease Cas9	A	1,056	Staphylococcus aureus	Mutation(s): 0  Gene Names: cas9 EC: 3.1
UniProt
Find proteins for J7RUA5 (Staphylococcus aureus) Explore J7RUA5  Go to UniProtKB:  J7RUA5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
sgRNA	B	99	Staphylococcus aureus

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Non-target DNA strand	C	43	Staphylococcus aureus

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Target DNA strand	D	43	Staphylococcus aureus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.17 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	Servalcat	0.4.66

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Omura, S.N., Nakagawa, R., Yamashita, K., Nishimasu, H., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	--
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release
  
• Version 1.1: 2026-04-15
  Changes: Data collection, Database references
• Version 1.2: 2026-04-29
  Changes: Data collection, Database references